Protein-nucleic acid interactions are important in a variety of biological control processes. In this investigation we propose to examine the role of RNA structure in specific protein recognition. Most of the study will center upon the "midivariant" of Q beta bacteriophage which self-replicates in vitro with Q beta replicase. This molecule is 218 nucleotides long and its conformation can be analyzed by temperature-jump relation kinetics, NMR, chemical modification and fluorescent probes. Subsequent to understanding the RNA conformation, singlet-singlet energy transfer will be used to monitor the replicase-RNA complex. In other experiments the conformation will be perturbed in well-defined ways and these changes will be correlated with the ability of the RNA to serve as template for RNA synthesis. One of the main questions to be answered is which aspects of primary sequence, secondary, or tertiary structure of the RNA are functionally important for binding of enzyme, initiation of synthesis, and replication. In addition, we will examine the effect of ethidium bromide on the conformation of midivariant mutants which replicate better in the presence of ethidium than the original midivariant. Analogous protein recognition studies will be performed on 5S ribosomal RNA and its binding proteins. tRNAs will be used in model system studies. The "midivariant" system is well-defined and therefore ideal for studying (a) the properties which provide an RNA molecule with its specificity to interact with enzymes and to replicate, (b) the manner in which an RNA template adjusts to selective environmental pressures, and (c) the effect of these changes on biological competence. Although this is a bacterial system, the results are a first step in facilitating our understanding of gene expression and replication in mammalian systems. Such detailed knowledge is, in turn, clearly vital if we are to understand both normal cell development and aberrant cellular processes such as observed in cancerous cells.